UC2-REST 0.2.0.28__tar.gz → 0.2.0.30__tar.gz

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: UC2-REST
-Version: 0.2.0.28
+Version: 0.2.0.30
 Summary: This pacage will help you to drive the ESP32-driven microscopy control modules from UC2
 Home-page: https://github.com/openUC2/UC2-REST
 Author: Benedict Diederich

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/UC2_REST.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: UC2-REST
-Version: 0.2.0.28
+Version: 0.2.0.30
 Summary: This pacage will help you to drive the ESP32-driven microscopy control modules from UC2
 Home-page: https://github.com/openUC2/UC2-REST
 Author: Benedict Diederich

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/UC2_REST.egg-info/SOURCES.txt

@@ -13,12 +13,14 @@ uc2rest/__init__.py
 uc2rest/__version__.py
 uc2rest/analog.py
 uc2rest/camera.py
+uc2rest/can.py
 uc2rest/cmdrecorder.py
 uc2rest/digitalout.py
 uc2rest/galvo.py
 uc2rest/gripper.py
 uc2rest/home.py
 uc2rest/laser.py
+uc2rest/lcddisplay.py
 uc2rest/ledmatrix.py
 uc2rest/logger.py
 uc2rest/message.py

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/UC2Client.py

@@ -9,6 +9,7 @@ from .mserial import Serial
 from .mserial import SerialManagerWrapper
 from .galvo import Galvo
 from .ledmatrix import LedMatrix
+from .lcddisplay import LCDDisplay
 from .motor import Motor
 from .gripper import Gripper
 from .home import Home
@@ -25,6 +26,7 @@ from .logger import Logger
 from .cmdrecorder import cmdRecorder
 from .temperature import Temperature
 from .message import Message
+from .can import CAN
 try:
     import requests
 except:
@@ -54,7 +56,7 @@ class UC2Client(object):
 
         you can send commands through wifi/http or usb/serial
         '''
-        if logger is None:
+        if True: #logger is None:
             self.logger = Logger()
         else:
             self.logger = logger
@@ -88,7 +90,7 @@ class UC2Client(object):
                         
         # import libraries depending on API version
         self.logger.debug("Using API version 2")        
-    
+
         # initialize state
         self.state = State(self)
 
@@ -98,9 +100,15 @@ class UC2Client(object):
         # initialize LED matrix
         self.led = LedMatrix(self, NLeds=NLeds)
 
+        # initialize LCD display
+        self.lcd = LCDDisplay(self)
+        
         # initilize motor
         self.motor = Motor(self)
         
+        # initialize CAN
+        self.can = CAN(self)
+        
         # initialize gripper
         self.gripper = Gripper(self)
         

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/__version__.py

@@ -6,7 +6,7 @@ __version__.py
 
 __title__ = 'UC2-REST'
 __description__ = 'This pacage will help you to drive the ESP32-driven microscopy control modules from UC2'
-__version__ = "v0.2.0.28"
+__version__ = "v0.2.0.30"
 __author__ = 'Benedict Diederich'
 __author_email__ = 'benedictdied@gmail.com'
 __license__ = 'GPL v3'

uc2_rest-0.2.0.30/uc2rest/can.py

@@ -0,0 +1,33 @@
+class CAN(object):
+    def __init__(self, parent):
+        """
+        CANController handles sending commands to a remote CAN device via the parent post_json interface.
+
+        :param parent: Parent object with post_json(path, payload, getReturn, timeout, nResponses)
+        """
+        self._parent = parent
+
+    def reboot_remote(self, qid=1, can_address=0, isBlocking=False, timeout=2):
+        """
+        Send a reboot signal to the remote CAN device.
+
+        :param qid: Query ID for the CAN command (default: 1)
+        :param isBlocking: If True, wait for response
+        :param timeout: Timeout for the command in seconds
+        :param can_address: Address of the CAN device to reboot (0 is master)
+        :return: Response from the device
+        """
+        path = "/can_act"
+        payload = {
+            "task": path,
+            "restart": int(can_address)
+        }
+        nResponses = 1 if isBlocking else 0
+        # Send the payload to the parent, which handles the actual communication
+        return self._parent.post_json(
+            path,
+            payload,
+            getReturn=isBlocking,
+            timeout=timeout if isBlocking else 0,
+            nResponses=nResponses
+        )

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/home.py

@@ -55,13 +55,14 @@ class Home(object):
                   endstoppolarity=endstoppolarity,
                   isBlocking=isBlocking)    
     
-    def home(self, axis=None, timeout=None, speed=None, direction=None, endposrelease=None, endstoppolarity=None, endstoptimeout=10000, isBlocking=False):
+    def home(self, axis=None, timeout=None, speed=None, direction=None, endposrelease=None, endstoppolarity=None, endstoptimeout=10000, isBlocking=False, preMove=True):
         '''
         axis = 0,1,2,3 or 'A, 'X','Y','Z'
         timeout => when to stop homing (it's a while loop on the MCU)
         speed => speed of homing (0...15000)
         direction => 1,-1 (left/right)
         endposrelease => how far to move after homing (0...3000)
+        preMove => the motor will first move by some steps in the opposite direction before homing, this is useful to avoid false triggering of the endstop
         '''
         
         # default values
@@ -79,6 +80,25 @@ class Home(object):
         if direction not in [-1,1]:
             direction = 1
 
+        if preMove:
+            # first move in the opposite direction
+            if direction == 1:
+                preMoveDirection = -1
+            else:
+                preMoveDirection = 1
+            
+            # move away from endstop
+            if axis == 1 or axis == "X":
+                self._parent.motor.move_x(steps=preMoveDirection*100, speed=self.speed, is_blocking=True, is_absolute=False, is_enabled=True)
+            elif axis == 2 or axis == "Y":
+                self._parent.motor.move_y(steps=preMoveDirection*100, speed=self.speed, is_blocking=True, is_absolute=False, is_enabled=True)
+            elif axis == 3 or axis == "Z":
+                self._parent.motor.move_z(steps=preMoveDirection*100, speed=self.speed, is_blocking=True, is_absolute=False, is_enabled=True)
+            elif axis == 0 or axis == "A":
+                self._parent.motor.move_a(steps=preMoveDirection*100, speed=self.speed, is_blocking=True, is_absolute=False, is_enabled=True)
+            else:   
+                raise ValueError("Invalid axis. Use 'X', 'Y', 'Z', or 'A'.")
+            time.sleep(0.5)
         # construct json string
         path = "/home_act"
 

uc2_rest-0.2.0.30/uc2rest/lcddisplay.py

@@ -0,0 +1,59 @@
+class LCDDisplay:
+    def __init__(self, parent):
+        """
+        LCD controller interface. 
+        Sends JSON commands to draw on the LCD via the parent object.
+        """
+        self._parent = parent
+        self.path = "/lcd_act"
+        self.timeout = 10
+        self.color = (255, 255, 255)  # Default color
+
+    def _send(self, action, isBlocking=True, **kwargs):
+        payload = {
+            "task": self.path,
+            "action": action,
+            **kwargs
+        }
+        return self._parent.post_json(self.path, payload, getReturn=isBlocking, nResponses=1, timeout=self.timeout)
+
+    def set_grating(self, perdiod, r=255, g=255, b=255, horizontal=True):
+        # {"task":"/lcd_act", "action":"gratingh","period":3,"r":255,"g":255,"b":255}
+        if horizontal:
+            return self._send("gratingh", period=perdiod, r=r, g=g, b=b)
+        else:
+            return self._send("gratingv", period=perdiod, r=r, g=g, b=b)
+        
+    def set_timeout(self, timeout=5):
+        """
+        Set the timeout for the LCD display.
+        :param timeout: Timeout in seconds.
+        """
+        self.timeout = timeout
+                
+    def set_color(self, r=255, g=255, b=255):
+        self.color = (r, g, b)
+
+    def clear(self, r=0, g=0, b=0):
+        return self._send("clear", r=r, g=g, b=b)
+
+    def hline(self, x, y, length, width=1):
+        r, g, b = self.color
+        # {"task":"/lcd_act","action":"hline","x":0,"y":10,"len":800,"width":1,"r":255,"g":255,"b":0}
+        return self._send("hline", x=x, y=y, len=length, width=width, r=r, g=g, b=b)
+
+    def vline(self, x, y, length, width=1):
+        r, g, b = self.color
+        return self._send("vline", x=x, y=y, len=length, width=width, r=r, g=g, b=b)
+
+    def point(self, x, y, diam=1):
+        r, g, b = self.color
+        return self._send("point", x=x, y=y, diam=diam, r=r, g=g, b=b)
+
+    def rect(self, x, y, len, width):
+        r, g, b = self.color
+        return self._send("rect", x=x, y=y, len=len, width=width, r=r, g=g, b=b)
+
+    def fill(self, x, y, len, width):
+        r, g, b = self.color
+        return self._send("fill", x=x, y=y, len=len, width=width, r=r, g=g, b=b)

uc2_rest-0.2.0.30/uc2rest/logger.py

@@ -0,0 +1,45 @@
+import logging
+
+
+class Logger(object):
+    def __init__(
+        self,
+        name=__name__,
+        log_to_file=False,
+        filename='uc2rest.log'
+    ):
+        # Create a logger with the given name
+        self.logger = logging.getLogger(name)
+        self.logger.setLevel(logging.DEBUG)
+        formatter = logging.Formatter(
+            '%(asctime)s [%(levelname)s] %(name)s: %(message)s'
+        )
+
+        # Console handler
+        ch = logging.StreamHandler()
+        ch.setLevel(logging.DEBUG)
+        ch.setFormatter(formatter)
+        self.logger.addHandler(ch)
+
+        # Optional file handler
+        if log_to_file:
+            fh = logging.FileHandler(filename)
+            fh.setLevel(logging.DEBUG)
+            fh.setFormatter(formatter)
+            self.logger.addHandler(fh)
+
+    def error(self, message):
+        # Log an error message
+        self.logger.error(message)
+
+    def debug(self, message):
+        # Log a debug message
+        self.logger.debug(message)
+
+    def info(self, message):
+        # Log an info message
+        self.logger.info(message)
+
+    def warning(self, message):
+        # Log a warning message
+        self.logger.warning(message)

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/motor.py

@@ -23,7 +23,6 @@ class Motor(object):
         self.minStep = np.ones((self.nMotors))*(-np.inf)
         self.currentDirection = np.zeros((self.nMotors))
         self.currentPosition = np.zeros((self.nMotors))
-        self._position = np.zeros((self.nMotors)) # position from the last motor status update
 
         self.minPosX = -np.inf
         self.minPosY = -np.inf
@@ -42,7 +41,7 @@ class Motor(object):
         self.offsetY = 0
         self.offsetZ = 0
 
-        self.DEFAULT_ACCELERATION = 10000
+        self.DEFAULT_ACCELERATION = 1000000
 
         self.motorAxisOrder = [0,1,2,3] # motor axis is 1,2,3,0 => X,Y,Z,T # FIXME: Hardcoded
 
@@ -84,9 +83,9 @@ class Motor(object):
             for iMotor in range(nSteppers):
                 stepperID = data["steppers"][iMotor]["stepperid"]
                 # FIXME:  smart to re-update this variable? Will be updated by motor-sender too
-                self._position[stepperID] = data["steppers"][iMotor]["position"] * stepSizes[stepperID] - offSets[stepperID]
+                self.currentPosition[stepperID] = data["steppers"][iMotor]["position"] * stepSizes[stepperID] - offSets[stepperID]
             if  callable(self._callbackPerKey[0]):
-                self._callbackPerKey[0](self._position) # we call the function with the value
+                self._callbackPerKey[0](self.currentPosition) # we call the function with the value
         except Exception as e:
             print("Error in _callback_motor_status: ", e)
 
@@ -142,6 +141,38 @@ class Motor(object):
     def setMotorAxisOrder(self, order=[0,1,2,3]):
         self.motorAxisOrder = order
 
+    # { "task": "/motor_act", "focusscan": { "zStart": 0, "zStep": 50, "nZ": 20, "tPre": 80, "tTrig": 20, "tPost": 0, "led": 0, "illumination": [0, 255, 0, 0], "speed": 20000, "acceleration": 1000000, "qid": 42 }}
+    def startFocusScanning(self, zStart=0, zStep=50, nZ=20, tPre=80, tTrig=20, tPost=0, led=0, illumination=[0, 255, 0, 0], speed=20000, acceleration=1000000, qid=42):
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "focusscan": {
+                "zStart": zStart,
+                "zStep": zStep,
+                "nZ": nZ,
+                "tPre": tPre,
+                "tTrig": tTrig,
+                "tPost": tPost,
+                "led": led,
+                "illumination": illumination,
+                "speed": speed,
+                "acceleration": acceleration,
+                "qid": qid
+            }
+        }
+        r = self._parent.post_json(path, payload)
+        return r
+    
+    def stopFocusScanning(self):
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "focusscan": {
+                "stopped": 1
+            }
+        }
+        r = self._parent.post_json(path, payload)
+        return r
     '''################################################################################################################################################
     HIGH-LEVEL Functions that rely on basic REST-API functions
     ################################################################################################################################################'''
@@ -423,7 +454,7 @@ class Motor(object):
                 self.currentDirection[iMotor] = np.sign(steps[iMotor])
             if self.lastDirection[iMotor] != self.currentDirection[iMotor]:
                 # we want to overshoot a bit
-                steps[iMotor] = steps[iMotor] +  self.currentDirection[iMotor]*self.backlash[iMotor]
+                steps[iMotor] = steps[iMotor] + self.currentDirection[iMotor]*self.backlash[iMotor]
 
     
             if isAbsoluteArray[iMotor]:
@@ -459,6 +490,10 @@ class Motor(object):
         motorPropList = []
         for iMotor in range(4):
             if isAbsoluteArray[iMotor] or abs(steps[iMotor])>0:
+                # if we are absolute and the last target position is the same as the current one, we don't need to move
+                if isAbsoluteArray[iMotor] and abs(steps[iMotor] - self.currentPosition[iMotor])<1:
+                    if self._parent.serial.DEBUG: self._parent.logger.debug(f"Motor {iMotor} is already at target position {steps[iMotor]}")
+                    continue
                 motorProp = { "stepperid": int(self.motorAxisOrder[iMotor]),
                              "position": int(steps[iMotor]),
                              "speed": int(speed[iMotor]),
@@ -471,7 +506,8 @@ class Motor(object):
                 else:
                     motorProp["accel"] = self.DEFAULT_ACCELERATION
                 motorPropList.append(motorProp)
-
+        if len(motorPropList)==0:
+            return "{'return':-1}"
         path = "/motor_act"
         payload = {
             "task":path,
@@ -617,9 +653,9 @@ class Motor(object):
         _physicalOffsets = np.array((self.offsetA, self.offsetX, self.offsetY, self.offsetZ))
 
         # this may be an asynchronous call.. #FIXME!
-        r = self._parent.post_json(path, payload, getReturn = True, nResponses=1, timeout=timeout)
+        r = self._parent.post_json(path, payload, getReturn = True, nResponses=1, timeout=timeout)[0]
         # returns {"motor": }
-        if "motor" in r:
+        if "motor" in r :
             for index, istepper in enumerate(r["motor"]["steppers"]):
                 if index >3: break # TODO: We would need to handle other values too soon
                 _position[istepper["stepperid"]]=istepper["position"]*_physicalStepSizes[self.motorAxisOrder[index]]-_physicalOffsets[self.motorAxisOrder[index]]
@@ -698,7 +734,72 @@ class Motor(object):
 
     def set_direction(self, axis=1, sign=1, timeout=1):
         return False
+    
+    def stop_stage_scanning(self):
+        # {"task":"/motor_act", "stagescan":{ "stopped":1 }}
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "stagescan": {
+                "stopped": 1
+            }
+        }
+        r = self._parent.post_json(path, payload)
+        return r
+    
+    
 
+    def start_stage_scanning(self, xstart=0, xstep=1000, nx=20, ystart=0, ystep=1000, ny=10, tsettle=5, tExposure=50, illumination=(0,0,0,0), led=0, speed=20000, acceleration=None):
+		#	{"task": "/motor_act", "stagescan": {"xStart": 0, "yStart": 0, "xStep": 500, "yStep": 500, "nX": 10, "nY": 10, "tPre": 50, "tPost": 50, "illumination": [0, 1, 0, 0], "led": 255}}
+        if acceleration is None:
+            acceleration = self.DEFAULT_ACCELERATION
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "stagescan": {
+                "xStart": xstart / self.stepSizeX,
+                "xStep": xstep / self.stepSizeX,
+                "nX": nx,
+                "yStart": ystart / self.stepSizeY,
+                "yStep": ystep / self.stepSizeY,
+                "nY": ny,
+                "tPre": tsettle,
+                "tPost": tExposure,
+                "illumination": illumination,
+                "led": led,
+                "accel": self.DEFAULT_ACCELERATION,  # default acceleration
+                "speed": speed,  # default speed
+            }
+        }
+        r = self._parent.post_json(path, payload)
+        return r
+    
+    def start_stage_scanning_by_coordinates(self, coordinates, tPre=50, tPost=50, led=100, illumination=[50, 75, 100, 125], stopped=0): 
+        '''
+        Example: {"task": "/motor_act", "stagescan": {"coordinates": [{"x": 100, "y": 200}, {"x": 300, "y": 400}, {"x": 500, "y": 600}], "tPre": 50, "tPost": 50, "led": 100, "illumination": [50, 75, 100, 125], "stopped": 0}}
+        
+        coordinates: list of dictionaries with x and y coordinates
+        tPre: time before exposure in ms
+        tPost: exposure time - time after action
+        led: led value for illumination
+        illumination: list of values for each channel of the illumination
+        stopped: 0 for start, 1 for stop
+        '''
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "stagescan": {
+                "coordinates": coordinates,
+                "tPre": tPre,
+                "tPost": tPost,
+                "led": led,
+                "illumination": illumination,
+                "stopped": stopped
+            }
+        }
+        r = self._parent.post_json(path, payload)
+        return r
+            
     def set_tmc_parameters(self, axis=0, msteps=None, rms_current=None, stall_value=None, sgthrs=None, semin=None, semax=None, blank_time=None, toff=None, timeout=1):
         ''' set the TMC parameters for a specific axis 
         msteps: microsteps

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/mserial.py

@@ -33,7 +33,7 @@ class Serial:
             self._logger.addHandler(logging.StreamHandler())
         else:
             self._logger = self._parent.logger
-
+        self.identifier_counter = 0 
         self.identity = identity
         self.DEBUG = DEBUG
         self.is_connected = False
@@ -228,7 +228,8 @@ class Serial:
         try:
             mLine = serialdevice.readline()
             if self.cmdReadCallBackFct is not None and mLine!=b'' and mLine != b'\n' :
-                self.cmdReadCallBackFct(mLine)  
+                try:self.cmdReadCallBackFct(mLine)  
+                except:pass
             return mLine
         except SerialException as e:
             self._logger.error("Failed to read the line in serial: "+str(e))
@@ -305,7 +306,7 @@ class Serial:
     def _process_commands(self):
         buffer = ""
         reading_json = False
-        currentIdentifier = None
+        currentIdentifier = 0
         nLineCountTimeout = 50 # maximum number of lines read before timeout
         lineCounter = 0
         nFailedCommands = 0
@@ -339,19 +340,20 @@ class Serial:
                     line = ""
                         
                     # if we have a problem with the serial connection, we need to reconnect
-                    for i in range(4):
-                        nFailedCommands=0
-                        if self.reconnect():
-                            self._logger.debug("Reconnected to the serial device")
-                            break
-                        else:
-                            self._logger.debug("Failed to reconnect to the serial device")
-                        time.sleep(1)
+                    if nFailedCommands>5:
+                        for i in range(4):
+                            nFailedCommands=0
+                            if self.reconnect():
+                                self._logger.debug("Reconnected to the serial device")
+                                break
+                            else:
+                                self._logger.debug("Failed to reconnect to the serial device")
+                            time.sleep(1)
                 
             if line == "++":
                 reading_json = True
                 continue
-            elif line.find("error") != -1:
+            elif line.find("error") != -1 and currentIdentifier is not None:
                 # if we have an error, we need to reset the last command
                 self._logger.debug("Error - last command did not match the firmware: "+str(self.commands[currentIdentifier]))
                 self.resetLastCommand = True
@@ -365,7 +367,7 @@ class Serial:
                 reading_json = False
                 try:
                     json_response = json.loads(buffer)
-                    self._logger.debug("[ProcessCommands]: "+str(json_response))
+                    if self.DEBUG: self._logger.debug("[ProcessCommands]: "+str(json_response))
                     if len(self.callBackList) > 0:
                         for callback in self.callBackList:
                             # check if json has key
@@ -385,9 +387,10 @@ class Serial:
                 except: pass
 
                 with self.lock:
-                    try:
+                    try: # TODO: THis looks fishy   an
                         self.responses[currentIdentifier].append(json_response.copy())
-                    except:
+                    except Exception as e:
+                        #self._logger.error("Failed to append the response: "+str(e))
                         self.responses[currentIdentifier] = list()
                         self.responses[currentIdentifier].append(json_response.copy())
                     buffer = ""      # reset buffer

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/objective.py

@@ -1,5 +1,6 @@
 import time
 import json
+import numpy as np
 
 class Objective(object):
     def __init__(self, parent):

{uc2_rest-0.2.0.28 → uc2_rest-0.2.0.30}/uc2rest/state.py

@@ -55,6 +55,7 @@ class State(object):
     
     def espRestart(self,timeout=1):
         # if isController =True=> only PS jjoystick will be accepted
+        # {"task":"/state_act", "restart":1}
         path = "/state_act"
         payload = {
             "restart":1

uc2_rest-0.2.0.28/uc2rest/logger.py

@@ -1,9 +0,0 @@
-class Logger(object):
-    def __init__(self):
-        pass
-
-    def error(self,message):
-        print(message)
-
-    def debug(self, message):
-        print(message)